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Related Concept Videos

RNA Structure01:23

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
RNA Structure01:19

RNA Structure

The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
RNA Structure01:23

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
Nucleic Acid Structure01:25

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...
Transfer RNA Synthesis02:36

Transfer RNA Synthesis

One of the unique features of tRNA is the presence of modified bases. In some tRNAs, modified bases account for nearly 20% of the total bases in the molecule. Altogether, these unusual bases protect the tRNA from enzymatic degradation by RNases.
Each of these chemical modifications is carried by a specific enzyme, post-transcription. All of these enzymes have unique base and site-specificity. Methylation, the most common chemical modification, is carried by at least nine different enzymes, with...
Pre-mRNA Processing: Modification of pre-mRNA Ends01:35

Pre-mRNA Processing: Modification of pre-mRNA Ends

In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a cap to the 5' end of the growing transcript. In this process, a 5' phosphate is replaced by modified guanosine that has a methyl group attached (7-methyl guanosine). This 5' cap helps the cell...

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Related Experiment Video

Updated: May 31, 2026

An Assay for Quantifying Protein-RNA Binding in Bacteria
07:02

An Assay for Quantifying Protein-RNA Binding in Bacteria

Published on: June 12, 2019

Structural basis for RNA 3'-end recognition by Hfq.

Evelyn Sauer1, Oliver Weichenrieder

  • 1Department of Biochemistry, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.

Proceedings of the National Academy of Sciences of the United States of America
|July 9, 2011
PubMed
Summary

The bacterial Hfq protein binds small regulatory RNAs (sRNAs) by recognizing their uridine-rich 3' ends. This specific interaction, crucial for gene regulation, involves direct contact with the 3' hydroxyl group.

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RNA Secondary Structure Prediction Using High-throughput SHAPE
13:42

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Related Experiment Videos

Last Updated: May 31, 2026

An Assay for Quantifying Protein-RNA Binding in Bacteria
07:02

An Assay for Quantifying Protein-RNA Binding in Bacteria

Published on: June 12, 2019

RNA Secondary Structure Prediction Using High-throughput SHAPE
13:42

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Area of Science:

  • Bacterial gene regulation
  • Molecular biology
  • RNA-protein interactions

Background:

  • The Hfq protein is essential for bacterial gene regulation via small RNAs (sRNAs).
  • Hfq's specific recognition of diverse sRNAs was not fully explained by known RNA-binding mechanisms.
  • Bacterial RNA transcripts often feature uridine-rich 3' ends due to Rho-independent termination.

Purpose of the Study:

  • To elucidate the mechanism behind Hfq's specific recognition of small regulatory RNAs.
  • To identify a distinct RNA-binding mode for Hfq.

Main Methods:

  • Isothermal titration calorimetry to measure binding affinity.
  • Crystal structure determination of the Hfq-RNA complex.
  • Analysis of Hfq interaction with full-length sRNA substrates.

Main Results:

  • A novel Hfq-RNA interaction mode was identified, involving direct recognition of the uridine-rich 3' end.
  • Nanomolar binding affinity was observed between Hfq and a hexauridine substrate.
  • The crystal structure revealed a constricted RNA backbone enabling direct contact with the 3' hydroxyl group, which is crucial for high-affinity binding.

Conclusions:

  • The 3' hydroxyl group of uridine-rich RNA ends is critical for high-affinity Hfq binding.
  • This interaction mode likely explains Hfq's general recognition of bacterial sRNAs.
  • Hfq's sequestration of RNA 3' ends impacts sRNA stability, turnover, and regulatory mechanisms.